S100A7

Chr 1

S100 calcium binding protein A7

Also known as: PSOR1, S100A7c

NCBI Gene: 6278 ENSG00000143556 UniProt: P31151 OMIM: 600353

The protein encoded by this gene is a member of the S100 family of proteins containing 2 EF-hand calcium-binding motifs. S100 proteins are localized in the cytoplasm and/or nucleus of a wide range of cells, and involved in the regulation of a number of cellular processes such as cell cycle progression and differentiation. S100 genes include at least 13 members which are located as a cluster on chromosome 1q21. This protein differs from the other S100 proteins of known structure in its lack of calcium binding ability in one EF-hand at the N-terminus. The protein is overexpressed in hyperproliferative skin diseases, exhibits antimicrobial activities against bacteria and induces immunomodulatory activities. [provided by RefSeq, Nov 2014]

GeneReviews OMIM Research

GeneReviews OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.55

LOEUF

Multiple*

Mechanism· predicted

📖

GeneReview available — S100A7

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.55LOEUF

pLI 0.453

Z-score 1.14

OE 0.00 (0.00–1.55)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.49Z-score

OE missense 1.18 (0.97–1.44)

69 obs / 58.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.00 (0.00–1.55)

0≤0.351.4

Missense OE?1.18 (0.97–1.44)

0≤0.61.4

Synonymous OE?1.13

0≤1.21.6

LoF obs/exp: 0 / 1.5Missense obs/exp: 69 / 58.5Syn Z: -0.50

Background carrier burden — how many people carry a rare variant somewhere in S100A7?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 340

138 rare PASS variants

Rare truncating (LoF)

1 in 23,000

13 rare PASS variants

Rare synonymous (reference)

1 in 1,100

61 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for S100A7. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 530	1 in 29,000
South Asian	~43k	1 in 320	≈ 1 in 43,000
Remaining (unassigned)	~30k	1 in 270	1 in 6,000
European (Finnish)	~27k	1 in 4,400	none seen
Admixed American	~22k	1 in 320	none seen
African / African American	~21k	1 in 360	1 in 2,800
East Asian	~20k	1 in 400	≈ 1 in 20,000
Ashkenazi Jewish	~13k	≈ 1 in 6,500	none seen
Middle Eastern	~2,884	1 in 260	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓